Do you have the full URL for the RebelFAQ site - Firefox is warning me against going to that URL, presumably because snipurl has been used for linking to some dodgy sites?

If you do a google search on "Focusing screen in Canon not aligned" or similar you will see that this is a fairly common issue, especially on the Rebel / xxx class models and I'm not sure there is much that can be done about correcting it I'm afraid.

You could use the frame of the focussing screen for lining up horizontals perhaps rather than relying on the AF points, as this should be aligned correctly even if the focussing screen with its etched AF points are slightly out.